threeML 2.4.3.dev1__tar.gz → 2.5.0.dev2__tar.gz

{threeml-2.4.3.dev1/threeML.egg-info → threeml-2.5.0.dev2}/PKG-INFO

@@ -1,28 +1,30 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: threeML
-Version: 2.4.3.dev1
+Version: 2.5.0.dev2
 Summary: The Multi-Mission Maximum Likelihood framework
-Home-page: https://github.com/threeml/threeML
-Author: Giacomo Vianello
-Author-email: giacomo.vianello@gmail.com
-License: BSD-3
+Author-email: Giacomo Vianello <io@tu.com>
+Maintainer-email: Niccolò Di Lalla <niccolo.dilalla@stanford.edu>, Nicola Omodei <nicola.omodei@stanford.edu>
+License-Expression: BSD-3-Clause
+Project-URL: Homepage, https://github.com/threeml/threeML
 Project-URL: Documentation, https://threeml.readthedocs.io
+Project-URL: Repository, https://github.com/threeML/threeML
 Project-URL: Bug Tracker, https://github.com/threeML/threeML/issues
 Project-URL: Source Code, https://github.com/threeML/threeML
-Keywords: Likelihood,Multi-mission,3ML,HAWC,Fermi,HESS,joint,fit,bayesian,multi-wavelength
+Keywords: Likelihood,Multi-mission,3ML,HAWC,Fermi,HESS,joint fit,bayesian,multi-wavelength
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Topic :: Scientific/Engineering :: Astronomy
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: POSIX
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Environment :: Console
+Requires-Python: >=3.9.0
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.16
 Requires-Dist: scipy>=1.4
 Requires-Dist: emcee>=3
 Requires-Dist: astropy
-Requires-Dist: matplotlib<3.9
+Requires-Dist: matplotlib
 Requires-Dist: uncertainties
 Requires-Dist: pyyaml>=5.1
 Requires-Dist: dill
@@ -45,13 +47,16 @@ Requires-Dist: colorama
 Requires-Dist: omegaconf
 Requires-Dist: ipywidgets
 Requires-Dist: rich
+Requires-Dist: packaging
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-codecov; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx>=1.4; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Requires-Dist: nbsphinx; extra == "docs"
 Requires-Dist: sphinx-autoapi; extra == "docs"
+Dynamic: license-file
 
 ![CI](https://github.com/threeML/threeML/workflows/CI/badge.svg?branch=master&event=push)
 [![Conda Build and Publish](https://github.com/threeML/threeML/actions/workflows/conda_build.yml/badge.svg)](https://github.com/threeML/threeML/actions/workflows/conda_build.yml)
@@ -150,7 +155,7 @@ Here is a highlight list of teams and their publications using 3ML.
 * [POLAR](https://www.astro.unige.ch/polar-2/?fbclid=IwAR0IxMxHtiXZyqc0A_kT1xKe9ASAk_VmfJpCEBr0HOhDG5eOHY7AE5TWHv8)
   * [The POLAR gamma-ray burst polarization catalog](https://ui.adsabs.harvard.edu/link_gateway/2020A&A...644A.124K/doi:10.1051/0004-6361/202037915)
 
-A full list of publications using 3ML is [here](https://ui.adsabs.harvard.edu/abs/2015arXiv150708343V/citations).
+A full list of publications using 3ML is [here](https://scixplorer.org/abs/2015arXiv150708343V/citations).
 
 ## Citing 
 If you find this package useful in you analysis, or the code in your own custom data tools, please cite:
@@ -172,5 +177,5 @@ The SVO Filter Profile Service. Rodrigo, C., Solano, E., Bayo, A. http://ivoa.ne
 The Filter Profile Service Access Protocol. Rodrigo, C., Solano, E. http://ivoa.net/documents/Notes/SVOFPSDAL/index.html
 
 
-<img src="https://www.nsf.gov/images/logos/NSF_4-Color_bitmap_Logo.png"  width="100"> ThreeML is supported by National Science Foundation (NSF) <img src="https://www.nsf.gov/images/logos/NSF_4-Color_bitmap_Logo.png"  width="100">
+<img src="https://nsf.widen.net/content/txvhzmsofh/png/NSF_Official_logo_High_Res_1200ppi.png?position=c&quality=80&x.portal_shortcode_generated=dnmqqhzz&x.collection_sharename=wc3fwkos&x.app=portals"  width="100"> ThreeML is supported by National Science Foundation (NSF) <img src="https://nsf.widen.net/content/txvhzmsofh/png/NSF_Official_logo_High_Res_1200ppi.png?position=c&quality=80&x.portal_shortcode_generated=dnmqqhzz&x.collection_sharename=wc3fwkos&x.app=portals"  width="100">
 

{threeml-2.4.3.dev1 → threeml-2.5.0.dev2}/README.md

@@ -95,7 +95,7 @@ Here is a highlight list of teams and their publications using 3ML.
 * [POLAR](https://www.astro.unige.ch/polar-2/?fbclid=IwAR0IxMxHtiXZyqc0A_kT1xKe9ASAk_VmfJpCEBr0HOhDG5eOHY7AE5TWHv8)
   * [The POLAR gamma-ray burst polarization catalog](https://ui.adsabs.harvard.edu/link_gateway/2020A&A...644A.124K/doi:10.1051/0004-6361/202037915)
 
-A full list of publications using 3ML is [here](https://ui.adsabs.harvard.edu/abs/2015arXiv150708343V/citations).
+A full list of publications using 3ML is [here](https://scixplorer.org/abs/2015arXiv150708343V/citations).
 
 ## Citing 
 If you find this package useful in you analysis, or the code in your own custom data tools, please cite:
@@ -117,5 +117,5 @@ The SVO Filter Profile Service. Rodrigo, C., Solano, E., Bayo, A. http://ivoa.ne
 The Filter Profile Service Access Protocol. Rodrigo, C., Solano, E. http://ivoa.net/documents/Notes/SVOFPSDAL/index.html
 
 
-<img src="https://www.nsf.gov/images/logos/NSF_4-Color_bitmap_Logo.png"  width="100"> ThreeML is supported by National Science Foundation (NSF) <img src="https://www.nsf.gov/images/logos/NSF_4-Color_bitmap_Logo.png"  width="100">
+<img src="https://nsf.widen.net/content/txvhzmsofh/png/NSF_Official_logo_High_Res_1200ppi.png?position=c&quality=80&x.portal_shortcode_generated=dnmqqhzz&x.collection_sharename=wc3fwkos&x.app=portals"  width="100"> ThreeML is supported by National Science Foundation (NSF) <img src="https://nsf.widen.net/content/txvhzmsofh/png/NSF_Official_logo_High_Res_1200ppi.png?position=c&quality=80&x.portal_shortcode_generated=dnmqqhzz&x.collection_sharename=wc3fwkos&x.app=portals"  width="100">
 

threeml-2.5.0.dev2/pyproject.toml

@@ -0,0 +1,138 @@
+[build-system]
+requires = ["setuptools", "wheel", "versioneer[toml]"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "threeML"
+dynamic = ["version"]
+description = "The Multi-Mission Maximum Likelihood framework"
+readme = "README.md"
+license = "BSD-3-Clause"
+license-files = ["LICENSE"]
+requires-python = ">=3.9.0"
+authors = [
+    {name = "Giacomo Vianello", email = "io@tu.com"}
+]
+maintainers = [
+	    {name = "Niccolò Di Lalla", email = "niccolo.dilalla@stanford.edu"},
+        {name = "Nicola Omodei", email = "nicola.omodei@stanford.edu"}
+]
+keywords = [
+    "Likelihood",
+    "Multi-mission", 
+    "3ML",
+    "HAWC",
+    "Fermi",
+    "HESS",
+    "joint fit",
+    "bayesian",
+    "multi-wavelength"
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Topic :: Scientific/Engineering :: Astronomy",
+    "Intended Audience :: Science/Research",
+    "Operating System :: POSIX",
+    "Programming Language :: Python :: 3.9",
+    "Environment :: Console",
+]
+dependencies = [
+    "numpy>=1.16",
+    "scipy>=1.4",
+    "emcee>=3",
+    "astropy",
+    "matplotlib",
+    "uncertainties",
+    "pyyaml>=5.1",
+    "dill",
+    "iminuit>=2.0",
+    "astromodels",
+    "astroquery",
+    "corner",
+    "pandas",
+    "requests",
+    "speclite>=0.11",
+    "ipython",
+    "ipyparallel",
+    "joblib",
+    "numexpr",
+    "dynesty",
+    "numba",
+    "numdifftools",
+    "tqdm>=4.56.0",
+    "colorama",
+    "omegaconf",
+    "ipywidgets",
+    "rich",
+    "packaging"
+]
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+    "pytest-codecov",
+]
+docs = [
+    "sphinx>=1.4",
+    "sphinx_rtd_theme",
+    "nbsphinx",
+    "sphinx-autoapi",
+]
+
+[project.urls]
+Homepage = "https://github.com/threeml/threeML"
+Documentation = "https://threeml.readthedocs.io"
+Repository = "https://github.com/threeML/threeML"
+"Bug Tracker" = "https://github.com/threeML/threeML/issues"
+"Source Code" = "https://github.com/threeML/threeML"
+
+[tool.setuptools]
+packages = [
+    "threeML",
+    "threeML.exceptions",
+    "threeML.bayesian",
+    "threeML.minimizer",
+    "threeML.utils",
+    "threeML.utils.OGIP",
+    "threeML.utils.spectrum",
+    "threeML.utils.polarization",
+    "threeML.utils.photometry",
+    "threeML.utils.time_series",
+    "threeML.utils.data_builders",
+    "threeML.utils.data_builders.fermi",
+    "threeML.utils.data_download",
+    "threeML.utils.data_download.Fermi_LAT",
+    "threeML.utils.data_download.Fermi_GBM",
+    "threeML.utils.fitted_objects",
+    "threeML.utils.statistics",
+    "threeML.plugins",
+    "threeML.classicMLE",
+    "threeML.catalogs",
+    "threeML.io",
+    "threeML.io.plotting",
+    "threeML.io.cern_root_utils",
+    "threeML.parallel",
+    "threeML.config",
+    "threeML.test",
+    "threeML.plugins.experimental",
+]
+include-package-data = true
+
+[tool.setuptools.package-data]
+threeML = ["threeML/data/*"]
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "threeML/_version.py"
+versionfile_build = "threeML/_version.py"
+tag_prefix = "v"
+parentdir_prefix = "threeML-"
+
+[tool.pytest.ini_options]
+markers = [
+    "slow: slow tests",
+]
+
+[tool.isort]
+profile = "black"

threeml-2.5.0.dev2/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{threeml-2.4.3.dev1 → threeml-2.5.0.dev2}/setup.py

@@ -1,45 +1,34 @@
 #!/usr/bin/env python
 
 import os
-import sys
-
-import glob
 
 from setuptools import setup
 
 import versioneer
 
-
 # This dynamically loads a module and return it in a variable.
 # Will use it for check optional dependencies
 
 
 def is_module_available(module_name):
-
     # Fast path: see if the module has already been imported.
 
     try:
-
         exec("import %s" % module_name)
 
     except ImportError:
-
         return False
 
     else:
-
         return True
 
 
 # Create list of data files
 def find_data_files(directory):
-
     paths = []
 
-    for (path, directories, filenames) in os.walk(directory):
-
+    for path, directories, filenames in os.walk(directory):
         for filename in filenames:
-
             paths.append(os.path.join("..", path, filename))
 
     return paths
@@ -96,8 +85,16 @@ setup(
         "bayesian",
         "multi-wavelength",
     ],
-    # NOTE: we use '' as package name because the extra_files already contain the full path from here
-    package_data={"": extra_files,},
+    # NOTE: we use '' as package name because the extra_files already contain the full
+    # path from here
+    package_data={
+        "threeML/": [
+            "data/*",
+        ],
+    },
+    #     package_data={
+    #         "": extra_files,
+    #     },
 )  # End of setup()
 
 # Check for optional dependencies
@@ -114,7 +111,6 @@ optional_dependencies = {
 }
 
 for dep_name in optional_dependencies:
-
     optional_dependencies[dep_name][0] = is_module_available(dep_name)
 
 # Now print the final messages
@@ -124,13 +120,10 @@ print("OPTIONAL FEATURES:")
 print("##################\n\n")
 
 for dep_name in optional_dependencies:
-
     if optional_dependencies[dep_name][0]:
-
         status = "available"
 
     else:
-
         status = "*NOT* available"
 
     print(" * %s is %s (%s)\n" % (dep_name, status, optional_dependencies[dep_name][1]))

{threeml-2.4.3.dev1 → threeml-2.5.0.dev2}/threeML/__init__.py

@@ -1,31 +1,36 @@
 # We import matplotlib first, because we need control on the backend
 # Indeed, if no DISPLAY variable is set, matplotlib 2.0 crashes (at the moment, 05/26/2017)
+import os
+import traceback
+import warnings
+
 import pandas as pd
 
 pd.set_option("display.max_columns", None)
 
-import os
-import traceback
-import warnings
 
 # Workaround to avoid a segmentation fault with ROOT and a CFITSIO issue
 # LEAVE THESE HERE BEFORE ANY THREEML IMPORT
 try:
     import ROOT
+
+    ROOT.__doc__
 except ImportError:
     pass
 try:
     import pyLikelihood
+
+    pyLikelihood.__doc__
 except ImportError:
     pass
 
 from pathlib import Path
 
-from threeML.io.logging import setup_logger
-
 # Import everything from astromodels
 from astromodels import *
 
+from .io.logging import setup_logger
+
 from .config import (
     threeML_config,
     show_configuration,
@@ -38,9 +43,7 @@ log.propagate = False
 if threeML_config["logging"]["startup_warnings"]:
     log.info("Starting 3ML!")
     log.warning("WARNINGs here are [red]NOT[/red] errors")
-    log.warning(
-        "but are inform you about optional packages that can be installed"
-    )
+    log.warning("but are inform you about optional packages that can be installed")
     log.warning(
         "[red] to disable these messages, turn off start_warning in your config file[/red]"
     )
@@ -57,14 +60,12 @@ if os.environ.get("DISPLAY") is None:
 
 # Import version (this has to be placed before the import of serialization
 # since __version__ needs to be defined at that stage)
-from ._version import get_versions
-
-__version__ = get_versions()["version"]
-del get_versions
+from . import _version
 
+__version__ = _version.get_versions()["version"]
 
 import traceback
-from importlib.machinery import SourceFileLoader
+import importlib.util
 
 # Finally import the serialization machinery
 from .io.serialization import *
@@ -101,32 +102,24 @@ except ImportError:
 
 
 def is_module_importable(module_full_path):
-
     try:
-
-        _ = SourceFileLoader("__", str(module_full_path)).load_module()
-
-    except:
-
+        spec = importlib.util.spec_from_file_location(
+            module_full_path.stem, module_full_path
+        )
+        if spec is None or spec.loader is None:
+            raise ImportError(f"Cannot load {module_full_path}")
+        module = importlib.util.module_from_spec(spec)
+        spec.loader.exec_module(module)
+        return True, module
+    except Exception:
         return False, traceback.format_exc()
 
-    else:
-
-        return True, "%s imported ok" % module_full_path
-
 
 plugins_dir = Path(__file__).parent / "plugins"
 
 found_plugins = plugins_dir.glob("*.py")
 
-# Filter out __init__
-
-# found_plugins = filter(lambda x: str(x).find("__init__") < 0, found_plugins)
-
-# Filter out __init__
-
-found_plugins = filter(lambda x: str(x).find("__init__") < 0, found_plugins)
-
+found_plugins = [f for f in plugins_dir.glob("*.py") if f.name != "__init__.py"]
 
 _working_plugins = {}
 _not_working_plugins = {}
@@ -134,10 +127,9 @@ _not_working_plugins = {}
 # Loop over each candidates plugins and check if it is importable
 
 for i, module_full_path in enumerate(found_plugins):
-
     plugin_name = module_full_path.stem
 
-    is_importable, failure_traceback = is_module_importable(module_full_path)
+    is_importable, result = is_module_importable(module_full_path)
 
     if not is_importable:
         if threeML_config.logging.startup_warnings:
@@ -147,89 +139,65 @@ for i, module_full_path in enumerate(found_plugins):
                 # custom_exceptions.CannotImportPlugin,
             )
 
-        _not_working_plugins[plugin_name] = failure_traceback
+        _not_working_plugins[plugin_name] = result
 
         continue
 
-    else:
-
-        # First get the instrument name
-        try:
-
-            exec(f"from threeML.plugins.{plugin_name} import __instrument_name")
-
-        except ImportError:
-
-            # This module does not contain a plugin, continue
-            continue
-
-        # Now import the plugin itself
+    # First get the instrument name
+    module = result
+    instrument_name = getattr(module, "__instrument_name", None)
+    if not instrument_name:
+        continue
 
-        import_command = (
-            f"from threeML.plugins.{plugin_name} import {plugin_name}"
+    try:
+        imported_plugin = importlib.import_module(f"threeML.plugins.{plugin_name}")
+        plugin_class = getattr(imported_plugin, plugin_name)
+        globals()[plugin_name] = plugin_class
+    except ImportError:
+        log.warning(
+            f"Could not import plugin {plugin_name}."
+            "Do you have the relative instrument software installed?"
         )
-
-        try:
-
-            exec(import_command)
-
-        except ImportError:
-
-            pass
-
-        else:
-
-            _working_plugins[__instrument_name] = plugin_name
-
+        continue
+    _working_plugins[instrument_name] = plugin_name
 
 # Now some convenience functions
 
 
 def get_available_plugins():
-    """
-    Print a list of available plugins
+    """Print a list of available plugins.
 
     :return:
     """
     print("Available plugins:\n")
 
     for instrument, class_name in _working_plugins.items():
-
         print(f"{class_name} for {instrument}")
 
 
 def _display_plugin_traceback(plugin):
     if threeML_config.logging.startup_warnings:
-        log.warning(
-            "#############################################################"
-        )
+        log.warning("#############################################################")
         log.warning("\nCouldn't import plugin %s" % plugin)
         log.warning("\nTraceback:\n")
         log.warning(_not_working_plugins[plugin])
-        log.warning(
-            "#############################################################"
-        )
+        log.warning("#############################################################")
 
 
 def is_plugin_available(plugin):
-    """
-    Test whether the plugin for the provided instrument is available
+    """Test whether the plugin for the provided instrument is available.
 
     :param plugin: the name of the plugin class
     :return: True or False
     """
 
     if plugin in _working_plugins.values():
-
         # FIXME
         if plugin == "FermipyLike":
-
             try:
-
                 _ = FermipyLike.__new__(FermipyLike, test=True)
 
             except:
-
                 # Do not register it
 
                 _not_working_plugins[plugin] = traceback.format_exc()
@@ -241,15 +209,12 @@ def is_plugin_available(plugin):
         return True
 
     else:
-
         if plugin in _not_working_plugins:
-
             _display_plugin_traceback(plugin)
 
             return False
 
         else:
-
             log.error(f"Plugin {plugin} is not known")
             raise RuntimeError()
 
@@ -272,23 +237,22 @@ from threeML.catalogs import (
     FermiGBMBurstCatalog,
     FermiGBMTriggerCatalog,
     FermiLATSourceCatalog,
-    FermiPySourceCatalog,
     FermiLLEBurstCatalog,
+    FermiPySourceCatalog,
     SwiftGRBCatalog,
 )
-
 from threeML.io import (
+    activate_logs,
+    activate_progress_bars,
     activate_warnings,
-    silence_warnings,
-    update_logging_level,
+    debug_mode,
+    loud_mode,
+    quiet_mode,
     silence_logs,
     silence_progress_bars,
-    activate_progress_bars,
+    silence_warnings,
     toggle_progress_bars,
-    quiet_mode,
-    loud_mode,
-    debug_mode,
-    activate_logs,
+    update_logging_level,
 )
 from threeML.io.plotting.light_curve_plots import plot_tte_lightcurve
 from threeML.io.plotting.model_plot import (
@@ -306,8 +270,8 @@ from threeML.io.uncertainty_formatter import interval_to_errors
 # import time series builder, soon to replace the Fermi plugins
 from threeML.utils.data_builders import *
 from threeML.utils.data_download.Fermi_GBM.download_GBM_data import (
-    download_GBM_trigger_data,
     download_GBM_daily_data,
+    download_GBM_trigger_data,
 )
 
 # Import the LAT data downloader
@@ -331,20 +295,18 @@ from .classicMLE.joint_likelihood_set import (
     JointLikelihoodSetAnalyzer,
 )
 from .classicMLE.likelihood_ratio_test import LikelihoodRatioTest
-
-# Now read the configuration and make it available as threeML_config
-
 from .data_list import DataList
+from .io import get_threeML_style, set_threeML_style
 from .io.calculate_flux import calculate_point_source_flux
-
-# Import the plot_style context manager and the function to create new styles
-
 from .parallel.parallel_client import parallel_computation
 
 # Added by JM. step generator for time-resolved fits
 from .utils.step_parameter_generator import step_generator
 
-from .io import get_threeML_style, set_threeML_style
+# Now read the configuration and make it available as threeML_config
+
+
+# Import the plot_style context manager and the function to create new styles
 
 
 # Import optical filters
@@ -364,13 +326,10 @@ var_to_check = ["OMP_NUM_THREADS", "MKL_NUM_THREADS", "NUMEXPR_NUM_THREADS"]
 
 
 for var in var_to_check:
-
     num_threads = os.environ.get(var)
 
     if num_threads is not None:
-
         try:
-
             num_threads = int(num_threads)
 
         except ValueError:
@@ -382,7 +341,6 @@ for var in var_to_check:
                 )
 
     else:
-
         if threeML_config.logging.startup_warnings:
             log.warning(
                 "Env. variable %s is not set. Please set it to 1 for optimal performances in 3ML"
@@ -394,4 +352,3 @@ for var in var_to_check:
 del os
 del Path
 del warnings
-del SourceFileLoader

{threeml-2.4.3.dev1 → threeml-2.5.0.dev2}/threeML/_version.py

@@ -1,19 +1,18 @@
 
-# This file was generated by 'versioneer.py' (0.18) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
 
-from __future__ import absolute_import
 import json
 
 version_json = '''
 {
- "date": "2024-09-11T16:28:56-0400",
+ "date": "2026-02-16T18:58:32-0800",
  "dirty": false,
  "error": null,
- "full-revisionid": "df578f0d4c5b2d572f6ca9388ce9060b608941e0",
- "version": "2.4.3.dev1"
+ "full-revisionid": "edfee2b64f8527908fb0d0f6e07f3d64e8c8ce4f",
+ "version": "2.5.0.dev2"
 }
 '''  # END VERSION_JSON